rs3851059

Positions:

• chr10-80270902-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.277 in 152,092 control chromosomes in the GnomAD database, including 6,054 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.28 (6054 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0360

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.42 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.277 AC: 42148 AN: 151974 Hom.: 6047 Cov.: 32

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.345

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.434

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.273

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.277 AC: 42174 AN: 152092 Hom.: 6054 Cov.: 32 AF XY: 0.282 AC XY: 20949 AN XY: 74348

Gnomad4 AFR AF: 0.205

Gnomad4 AMR AF: 0.272

Gnomad4 ASJ AF: 0.285

Gnomad4 EAS AF: 0.435

Gnomad4 SAS AF: 0.363

Gnomad4 FIN AF: 0.312

Gnomad4 NFE AF: 0.298

Gnomad4 OTH AF: 0.273

Alfa AF: 0.297 Hom.: 13767

Bravo AF: 0.271

Asia WGS AF: 0.384 AC: 1332 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	7.2
DANN	Benign	0.42

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs3851059; hg19: chr10-82030658;